Multilayer Network - Visualization 0 - Plotting 3D networks

• To plot a Multilayer Network, we need a 3D space. For a 'step 0', we start by symple plotting 3D networks.
• This notebook expands the following content: https://deepnote.com/@deepnote/3D-network-visualisations-using-plotly-a18c5e37-a517-4b27-bfde-1fee94a5760f
• Overall, to plot a 3D network, we plot a 3D Scatter Plot to position the nodes and then add lines (edges) between points (nodes)
• Here I present a simplified version of the above tutorial, generalizing the code by adding functions.

import networkx as nx 
import plotly.graph_objects as plot3D
import pandas as pd
import numpy as np

def getTracesWithNodeInfo(G,nodeCommunity=False):
    if not nodeCommunity:
        nodeCommunity=[1 for n in range(G.number_of_nodes()+1)]
        
    spring_3D = nx.spring_layout(G,dim=3, seed=18)
    #we need to seperate the X,Y,Z coordinates for Plotly
    x_nodes = [spring_3D[i][0] for i in range(G.number_of_nodes())]# x-coordinates of nodes
    y_nodes = [spring_3D[i][1] for i in range(G.number_of_nodes())]# y-coordinates
    z_nodes = [spring_3D[i][2] for i in range(G.number_of_nodes())]# z-coordinates
    #We also need a list of edges to include in the plot
    edge_list = G.edges()
    
    #we  need to create lists that contain the starting and ending coordinates of each edge.
    x_edges=[]
    y_edges=[]
    z_edges=[]
    #need to fill these with all of the coordiates
    for edge in edge_list:
        #format: [beginning,ending,None]
        x_coords = [spring_3D[edge[0]][0],spring_3D[edge[1]][0],None]
        x_edges += x_coords

        y_coords = [spring_3D[edge[0]][1],spring_3D[edge[1]][1],None]
        y_edges += y_coords

        z_coords = [spring_3D[edge[0]][2],spring_3D[edge[1]][2],None]
        z_edges += z_coords

    #create a trace for the edges
    trace_edges = plot3D.Scatter3d(x=x_edges,
                            y=y_edges,
                            z=z_edges,
                            mode='lines',
                            line=dict(color='black', width=2),
                            hoverinfo='none')
    
    #create a trace for the nodes
    trace_nodes = plot3D.Scatter3d(x=x_nodes,
                            y=y_nodes,
                            z=z_nodes,
                            mode='markers',
                            marker=dict(symbol='circle',
                                        size=10,
                                        color=nodeCommunity, #color the nodes according to their community
                                        colorscale='Viridis', #either green or mageneta
                                        line=dict(color='black', width=0.5)),
                            text=list(G.nodes()),
                            hoverinfo='text')
    return [trace_edges,trace_nodes]

def getLayout(plotName):
    #we need to set the axis for the plot 
    axis = dict(showbackground=False,
                showline=False,
                zeroline=False,
                showgrid=False,
                showticklabels=False,
                showspikes=False,
                title='')

    #also need to create the layout for our plot
    layout = plot3D.Layout(title=plotName,
                    showlegend=False,
                    width=1024,
                    height=980,
                    scene=dict(xaxis=dict(axis),
                            yaxis=dict(axis),
                            zaxis=dict(axis),
                            ),
                    hovermode='closest')
    return layout

def plot3Dnetwork(G,name,nodeCommunity=False):
    data = getTracesWithNodeInfo(G,nodeCommunity)
    fig = plot3D.Figure(data=data, layout=getLayout(name))
    fig.show()

Simplified version of the tutorial

ZKC_graph = nx.karate_club_graph()
eachNodeCommunity = [1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

plot3Dnetwork(ZKC_graph,"Zachary's Karate Club - With Communities",eachNodeCommunity)

Zachary's Karate Club Without Communities

ZKC_graph = nx.karate_club_graph()
plot3Dnetwork(ZKC_graph,"Zachary's Karate Club")

Other Examples

G = nx.barbell_graph(6,2)
plot3Dnetwork(G,"Barbell")

G = nx.dodecahedral_graph()
plot3Dnetwork(G,"Dodecahedral")

G = nx.tutte_graph()
plot3Dnetwork(G,"Tutte")

G = nx.complete_graph(25)
plot3Dnetwork(G,"Complete")